package pacBiopackage;

import java.util.HashMap;
import java.util.List;

public class PacBioReadContainer  
{
	private String header=null;
	private String orginalSequence = null;
	private StringBuilder correctedSequence = null;
	private List<Integer> notCorrectedPositions = null;
	private HashMap<Integer, Boolean> checked = null;
	private List<Integer>frameShifts =null;
		
	public String getHeader() {
		return header;
	}
	public void setHeader(String header) {
		this.header = header;
	}
	public List<Integer> getPositionsList() {
		return notCorrectedPositions;
	}
	public void setNotCorrectedPositions(List<Integer> notCorrectedPositions) {
		this.notCorrectedPositions = notCorrectedPositions;
	}
	public String getOrginalSequence() {
		return orginalSequence;
	}
	public void setOrginalSequence(String orginalSequence) {
		this.orginalSequence = orginalSequence;
	}
	public StringBuilder getCorrectedSequence() {
		return correctedSequence;
	}
	public void setCorrectedSequence(StringBuilder correctedSequence) {
		this.correctedSequence = correctedSequence;
	}
	public HashMap<Integer, Boolean> getChecked() {
		return checked;
	}
	public void setChecked(HashMap<Integer, Boolean> checked) {
		this.checked = checked;
	}
	@Override
	public String toString() 
	{
		StringBuffer sb = new StringBuffer();
		sb.append(header+"\n"+ orginalSequence + "\n"+this.correctedSequence+"\n"+ this.notCorrectedPositions.toString()+"\n");
		return sb.toString();
	}
	public List<Integer> getFrameShifts() {
		return frameShifts;
	}
	public void setFrameShifts(List<Integer> frameShifts) {
		this.frameShifts = frameShifts;
	}
	
	public String toString(boolean flag)
	{
		if(!flag)
		return toString();
		else
		{
			StringBuffer sb = new StringBuffer();
			sb.append(header+"\n"+ orginalSequence + "\n"+this.correctedSequence+"\n");
			return sb.toString();
		}
	}
	
	
}
